Gopinath had been scheduled to leave the global lender to return to Harvard University in January, but decided to stay on in the wide-ranging policy role under IMF Managing Director Kristalina Georgieva, the IMF said.
Georgieva said Gopinath was "universally recognized as one of the world's leading macroeconomists" and had precisely the expertise needed for the No. 2 job, given the increased macroeconomic challenges facing IMF member countries as a result of the COVID-19 pandemic.
"Indeed, her particular skill set -- combined with her years of experience at the Fund as Chief Economist - make her uniquely well qualified. She is the right person at the right time," Georgieva said.
She said the IMF would realign some roles and responsibilities in its senior management team, with Gopinath to oversee surveillance activities, and research and flagship publications, while working to "foster the highest quality standards for Fund publications."
The United States, the largest shareholder in the IMF, welcomed the pick of Gopinath, and the move to restore job responsibilities that had been shifted under Okamoto, a source familiar with Treasury's thinking said.
Gopinath, the first woman to serve as the fund's chief economist, has played a key role in broadening the role of the IMF's research department, creating a new analytical approach to help countries respond to international capital flows, and also worked on a detailed IMF plan to end the pandemic, she said.
Okamoto said he would return to the private sector after over a decade of "intensive public service," but gave no details about his next position.
A dual citizen of the United States and India, Gopinath is due to start her new role on Jan. 21, shortly after the IMF releases an update to its World Economic Outlook. The IMF board is expected to approve the move in coming weeks.
The leadership changes come on the heels of an independent report commissioned by the World Bank, which claimed Georgieva, then the CEO of the World Bank, and other senior officials had pressured World Bank staff to alter data to favor China.
The IMF executive board cleared Georgieva of any wrongdoing in October, but U.S. Treasury Secretary Janet Yellen said Washington viewed the allegations as legitimate and serious, and demanded the IMF take proactive steps to ensure the integrity of IMF data and protection of any whistleblowers.
(Reporting by David Lawder and Andrea Shalal; additional reporting by Chris Gallagher; Editing by Marguerita Choy)
By Andrea Shalal and David Lawder